2W6X

Crystal structure of Sperm Whale Myoglobin mutant YQRF in complex with Xenon


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.72.8M AMMONIUM SULFATE, 0.1M TRIS/HCL, PH8.7, HANGING DROP AT RT
Crystal Properties
Matthews coefficientSolvent content
2.455

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.781α = 90
b = 90.781β = 90
c = 45.279γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2000-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7329.71000.0815.48.421861214.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.9599.90.036.47.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NAZ1.7329.752073911181000.1610.1590.195RANDOM13.33
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.239
r_dihedral_angle_4_deg18.691
r_dihedral_angle_3_deg12.496
r_dihedral_angle_1_deg4.479
r_scangle_it3.817
r_scbond_it2.481
r_mcangle_it1.501
r_angle_refined_deg1.165
r_mcbond_it0.859
r_symmetry_hbond_refined0.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.239
r_dihedral_angle_4_deg18.691
r_dihedral_angle_3_deg12.496
r_dihedral_angle_1_deg4.479
r_scangle_it3.817
r_scbond_it2.481
r_mcangle_it1.501
r_angle_refined_deg1.165
r_mcbond_it0.859
r_symmetry_hbond_refined0.496
r_nbtor_refined0.305
r_nbd_refined0.21
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.116
r_chiral_restr0.073
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1235
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing